Agts. Mulder, Scully, Kinsley, and Stonecypher were driving through Leon County, Florida, en route to a Bureau seminar in teamwork and communication, when they were stopped at a police checkpoint by state troopers investigating the disappearance of a man identified as Michael Asekoff. That morning, Mr. Asekoff and his son Louis had encountered an abandoned surveying transit while hunting in the woods. Their dog had led them to the blood-soaked jacket of one of two surveyors, identified as Michael Sloan and Marty Fox, who, unbeknownst to the Asekoffs, had disappeared a day earlier, after encountering an unidentified creature while conducting a survey for a projected real estate development. Mr. Asekoff loaded his shotgun and ordered Louis Asekoff to take the dog and flee the forest. As Louis Asekoff was complying with those instructions, he heard shots fired.

At the search-and-rescue checkpoint, Agt. Mulder left the other agents and spoke first to Mrs. Asekoff, wife of the missing man, and then to search-and-rescue team leader Michele Fazekas, to whom he identified himself as a Bureau agent. Officer Fazekas informed Agt. Mulder that she was unable to identify as human or animal the tracks that had been found near the site of the surveyors' disappearance. During that conversation, Agt. Mulder was joined by Agt. Scully. Agt. Kinsley meanwhile pointed out to Agt. Stonecypher a tree stump exhibit, showing that the tree had been standing for twenty years before Ponce de Leon had arrived in Florida. Agts. Mulder and Scully decided to remain in the area to investigate the disappearances.

That night, in his motel room, Agt. Mulder conducted online research into animal attacks, using his laptop computer. Agt. Scully joined Agt. Mulder in his room, offering him cheese and alcoholic beverages-despite such fraternization being, as Agt. Scully noted, contrary to Bureau regulations. Agt. Mulder stressed for Agt. Scully the fact that no known animal native to North America will attack the strongest among its prey and leave the weakest to escape. He suggested that the reported disappearances might represent a primitive culling technique. Agt. Mulder pointed out that the forest in which the disappearance had taken place is the oldest in the South. He then left the motel.

Meanwhile, in Louis Asekoff's bedroom on the second story of the Asekoff home, Mrs. Asekoff attempted to reassure Louis Asekoff of Mr. Asekoff's chances for a safe return home. She then proceeded to the first floor and turned out the lights for the night. Later, awakened by her dog's insistent barking, she let the dog out and followed the dog outside. The dog ran into some nearby bushes; when Mrs. Asekoff searched for him there, the dog snapped at her. Attempting to return to the house, Mrs. Asekoff found herself locked out. Louis Asekoff, awakened by his mother's shouts, observed an unidentifiable humanoid creature approaching him. Louis Asekoff fled the house through the small, swinging pet door at the side of the house, apparently pursued by the unidentified creature. Once outside he encountered Agt. Mulder.

After the arrival of local law enforcement at the Asekoff home, Louis Asekoff reported to Agts. Mulder and Scully and local law enforcement that he had seen an unidentified creature in the house and that the creature had red, glowing eyes. Agt. Scully suggested privately to Agt. Mulder that Louis Asekoff had been influenced by viewing on videotape the film "The Invisible Man," a copy of which she had discovered in his VCR. Agt. Mulder showed Agt. Scully tracks by the front door of the house that showed weight distribution more animal than human. Officer Fazekas confirmed Agt. Mulder's analysis of the tracks. Agt. Mulder urgently expressed his view that unless the creature was found, more attacks would ensue.

The next morning, Agts. Mulder and Scully, Officer Fazekas, and a technician identified as Jeff Glaser entered the Appalachicola National Forest with the intention of tracking the creature. Glaser made use of a Forward Looking Infrared (FLIR) electronic tracking device that detects body heat at three hundred yards. While Officer Fazekas gave the others communication and survival instructions, Agt. Scully learned via cell phone that local law enforcement was focusing its efforts on finding a drifter wanted for a double homicide in Alabama. Agt. Mulder outlined for Agt. Scully his hypothesis that some force in the forest was attempting to divide and conquer its enemy, which, Agt. Mulder suggested, the force might construe as people involved in the projected real-estate property currently under development on the forest land.

As the team moved through the forest, Officer Fazekas left a trail of white stones. Glaser noted that the absence of wildlife that morning was unusual. Shortly after, the FLIR device registered the presence of one and then two bodies in motion, moving through the forest in opposite directions. The team rapidly split into two parties and attempted to track the creatures, Agt. Mulder and Glaser pursuing one, Agt. Scully and Officer Fazekas the other. After a short pursuit, Glaser reported to Agt. Mulder that the creature's presence was no longer registered on the FLIR screen; meanwhile Agt. Scully pointed out to Officer Fazekas that the creature might intentionally be dividing the team. As Agt. Scully and Officer Fazekas were attempting to return to Agt. Mulder and Glaser, Officer Fazekas suddenly fell and disappeared. Agt. Scully called for Agt. Mulder. Agt. Mulder and Glaser responded to her call. Agt. Mulder suggested that because Officer Fazekas had been leading the team, the creatures had perceived her as the strongest and therefore targeted her first. He urged prompt action in order to locate Officer Fazekas. Glaser argued for a retreat. Agt. Scully, noting their lack of food, water, and support personnel, agreed with Glaser.

Proceeding with caution, the team retraced its steps. The agents discussed the biological possibility that the creatures might regulate their body temperatures, thus eluding FLIR. Agt. Mulder described for Agt. Scully the contents of an X-File dating back to 1952 that contains reports of attacks by "moth men," primitive in appearance, with red, glowing eyes, allegedly seen in Point Pleasant, West Virgina. As the group attempted to follow their trail out of the forest, Glaser noted the absence of the white stones with which Officer Fazekas had created a trail. Agt. Scully noted the presence of something moving in the woods. She and Agt. Mulder drew their weapons. The forest had again become silent. Glaser located the creature on the FLIR screen. With Glaser's assistance, Agt. Mulder observed the creature and pursued it, firing his weapon. Agt. Scully also fired her weapon. As Glaser fled the scene, he fell and disappeared in the same manner as Officer Fazekas. Agt. Mulder counted the shots he and Agt. Scully had fired and noted the scarcity of ammunition. Agt. Mulder then appeared to fall and disappear from view as the others had done. Agt. Scully located Agt. Mulder struggling with an unidentified assailant in a bush and fired toward him, apparently scaring the assailant into retreat. Agt. Mulder was beaten and bleeding, but largely unhurt.

The agents made camp. As night fell and Agt. Scully attempted to start a fire, they discussed death, cartoon characters, and the reports of "moth men." As Agt. Mulder fell asleep, Agt. Scully sang a song in response to Agt. Mulder's request. Meanwhile red, glowing eyes appeared in a nearby tree, but did not approach the agents..

The next morning, shortly after Agt. Mulder awakened, Agt. Scully fell into a hole, which she discovered to be a large underground chamber. There she found Officer Fazekas, the two surveyors, Mr. Asekoff, and several unidentified others, tied to poles. With the exception of Fazekas, all appeared to be deceased. Agt. Scully diagnosed Officer Fazekas' condition as extremely critical. She described the situation to Agt. Mulder, who remained outside the chamber opening. Realizing she was not alone in the chamber, she informed Agt. Mulder that she did not have her weapon. Agt. Mulder dropped his weapon down to her, and then, on seeing something approach him, leapt into the chamber as well. In the chamber, Agt. Scully fired on the creature as it charged her, apparently killing it. The agents observed the deceased creature to be gnarled, woody, and tree-like. They removed Officer Fazekas and others from the poles, in which were carved the words "ad noctum."

Agts. Kinsley and Stonecypher then arrived at the scene, accompanied by a search team. The bodies were removed; Mr. Asekoff was also determined to be alive. At the site where they had first encountered the police checkpoint, Agts. Mulder and Kinsley discussed the case. Agt. Mulder explained that the Latin words "ad noctum," which translated to "into darkness," are known to have been carved by the Spanish conquistadors into poles to which they lashed their native captives. Agt. Kinsley expressed skepticism that the creatures were connected with the conquistadors. Agt. Stonecypher reported that neither Glaser nor the second predator had been found. The agents discussed the possibility that the creature had entered the Asekoff home because it would follow and attack anyone who had been in the woods and encroached its territory. Agt. Mulder then became concerned as to the whereabouts of Agt. Scully, who had proceeded to the motel.

Agt. Mulder quickly drove to the motel and found Agt. Scully unhurt, having packed their bags. As Agts. Mulder and Scully left the motel, leaving behind a creature with red, glowing eyes lurking under the bed.